Cell Ranger DNA Output

The cellranger-dna pipeline will generate .dloupe files that can be found in the outs folder of a completed run.

Gene-specific functionality, such as searching by gene and viewing gene annotations in the trace, is only available if the reference supplied to cellranger-dna contains gene annotations in a GTF format. For more information on how annotations in the GTF file make it into the Loupe file, consult the cellranger-dna mkref documentation.

The .dloupe file encodes the same tree structure, copy numbers and heterogeneity as the other output files in the pipeline. However, the file stores a quantized, approximated read depth per bin in order to save disk space. For more information, see Technical Details.

Information Exclusive to the Web Summary View

You will still need to consult the Cell Ranger DNA run summary file to view quality control data and other metadata about a particular run; this is not available in Loupe scDNA Browser.

Keeping Local Copies

It is highly recommended that you copy the .dloupe file from the pipeline outs folder onto the machine where you will run Loupe scDNA Browser. Loupe scDNA Browser makes heavy use of disk I/O, so it will run faster if your file is on a local drive as opposed to on a mounted network share. Typical .dloupe files consume about 250-300KB of disk space per cell, though that figure also depends on copy number variability and genome size.